HEADER HYDROLASE 29-NOV-21 7W4Y TITLE CRYSTAL STRUCTURE OF PDE4D CATALYTIC DOMAIN COMPLEXED WITH 33A COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4D; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DPDE3,PDE43; COMPND 5 EC: 3.1.4.53; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PDE4D, DPDE3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS CAMP-SPECIFIC 3', 5'-CYCLIC PHOSPHODIESTERASE 4D, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.-Y.HUANG,H.-B.LUO REVDAT 3 29-NOV-23 7W4Y 1 REMARK REVDAT 2 23-MAR-22 7W4Y 1 JRNL REVDAT 1 16-MAR-22 7W4Y 0 JRNL AUTH Z.SONG,Y.Y.HUANG,K.Q.HOU,L.LIU,F.ZHOU,Y.HUANG,G.WAN,H.B.LUO, JRNL AUTH 2 X.F.XIONG JRNL TITL DISCOVERY AND STRUCTURAL OPTIMIZATION OF TODDACOUMALONE JRNL TITL 2 DERIVATIVES AS NOVEL PDE4 INHIBITORS FOR THE TOPICAL JRNL TITL 3 TREATMENT OF PSORIASIS. JRNL REF J.MED.CHEM. V. 65 4238 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 35188767 JRNL DOI 10.1021/ACS.JMEDCHEM.1C02058 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 45654 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.917 REMARK 3 FREE R VALUE TEST SET COUNT : 2245 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 24.1800 - 5.2745 0.97 2825 143 0.1700 0.2020 REMARK 3 2 5.2745 - 4.1937 0.99 2775 142 0.1570 0.2029 REMARK 3 3 4.1937 - 3.6656 0.99 2718 154 0.1680 0.2117 REMARK 3 4 3.6656 - 3.3314 0.99 2706 142 0.1861 0.2369 REMARK 3 5 3.3314 - 3.0931 0.99 2696 154 0.2012 0.2378 REMARK 3 6 3.0931 - 2.9111 1.00 2724 135 0.1989 0.2866 REMARK 3 7 2.9111 - 2.7655 1.00 2720 134 0.2051 0.2460 REMARK 3 8 2.7655 - 2.6453 1.00 2697 152 0.2029 0.2317 REMARK 3 9 2.6453 - 2.5436 1.00 2699 136 0.2090 0.2476 REMARK 3 10 2.5436 - 2.4559 1.00 2701 134 0.2349 0.2823 REMARK 3 11 2.4559 - 2.3792 1.00 2709 130 0.2066 0.2384 REMARK 3 12 2.3792 - 2.3112 1.00 2685 131 0.2261 0.2484 REMARK 3 13 2.3112 - 2.2504 1.00 2691 134 0.2513 0.3215 REMARK 3 14 2.2504 - 2.1955 1.00 2704 138 0.2312 0.2886 REMARK 3 15 2.1955 - 2.1457 1.00 2663 146 0.2255 0.2939 REMARK 3 16 2.1457 - 2.1000 1.00 2696 140 0.2250 0.3064 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.211 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.263 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 5399 REMARK 3 ANGLE : 0.938 7344 REMARK 3 CHIRALITY : 0.047 843 REMARK 3 PLANARITY : 0.004 938 REMARK 3 DIHEDRAL : 18.996 1986 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7W4Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1300025992. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-APR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER AXIOM 200 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO 171.39.46 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45663 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 24.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.21200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 5WQA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES (PH 7.4), 0.1 M MGCL2, 15% REMARK 280 PEG3350, 10% ISOPROPANOL, 25% ETHYLENE GLYCOL, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 29.14700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 81.71150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.41700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 81.71150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.14700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.41700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 78 REMARK 465 ILE A 79 REMARK 465 PRO A 80 REMARK 465 ARG A 81 REMARK 465 PHE A 82 REMARK 465 GLY A 83 REMARK 465 VAL A 84 REMARK 465 LYS A 85 REMARK 465 THR A 86 REMARK 465 GLU A 87 REMARK 465 GLN A 412 REMARK 465 SER A 413 REMARK 465 PRO A 414 REMARK 465 SER A 415 REMARK 465 PRO A 416 REMARK 465 ALA A 417 REMARK 465 PRO A 418 REMARK 465 ASP A 419 REMARK 465 ASP A 420 REMARK 465 PRO A 421 REMARK 465 GLU A 422 REMARK 465 GLU A 423 REMARK 465 GLY A 424 REMARK 465 ARG A 425 REMARK 465 GLN A 426 REMARK 465 GLY A 427 REMARK 465 GLN A 428 REMARK 465 THR A 429 REMARK 465 GLU A 430 REMARK 465 LYS A 431 REMARK 465 PHE A 432 REMARK 465 GLN A 433 REMARK 465 PHE A 434 REMARK 465 GLU A 435 REMARK 465 LEU A 436 REMARK 465 THR A 437 REMARK 465 LEU A 438 REMARK 465 GLU A 439 REMARK 465 GLU A 440 REMARK 465 ASP A 441 REMARK 465 GLY A 442 REMARK 465 GLU A 443 REMARK 465 SER A 444 REMARK 465 ASP A 445 REMARK 465 THR A 446 REMARK 465 GLU A 447 REMARK 465 LYS A 448 REMARK 465 ASP A 449 REMARK 465 ALA A 450 REMARK 465 SER B 78 REMARK 465 ILE B 79 REMARK 465 PRO B 80 REMARK 465 ARG B 81 REMARK 465 PHE B 82 REMARK 465 GLY B 83 REMARK 465 VAL B 84 REMARK 465 LYS B 85 REMARK 465 THR B 86 REMARK 465 GLU B 87 REMARK 465 GLN B 88 REMARK 465 GLN B 412 REMARK 465 SER B 413 REMARK 465 PRO B 414 REMARK 465 SER B 415 REMARK 465 PRO B 416 REMARK 465 ALA B 417 REMARK 465 PRO B 418 REMARK 465 ASP B 419 REMARK 465 ASP B 420 REMARK 465 PRO B 421 REMARK 465 GLU B 422 REMARK 465 GLU B 423 REMARK 465 GLY B 424 REMARK 465 ARG B 425 REMARK 465 GLN B 426 REMARK 465 GLY B 427 REMARK 465 GLN B 428 REMARK 465 THR B 429 REMARK 465 GLU B 430 REMARK 465 LYS B 431 REMARK 465 PHE B 432 REMARK 465 GLN B 433 REMARK 465 PHE B 434 REMARK 465 GLU B 435 REMARK 465 LEU B 436 REMARK 465 THR B 437 REMARK 465 LEU B 438 REMARK 465 GLU B 439 REMARK 465 GLU B 440 REMARK 465 ASP B 441 REMARK 465 GLY B 442 REMARK 465 GLU B 443 REMARK 465 SER B 444 REMARK 465 ASP B 445 REMARK 465 THR B 446 REMARK 465 GLU B 447 REMARK 465 LYS B 448 REMARK 465 ASP B 449 REMARK 465 ALA B 450 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 812 O HOH A 850 2.06 REMARK 500 O HOH A 719 O HOH A 850 2.07 REMARK 500 O HOH A 771 O HOH A 812 2.09 REMARK 500 O HOH B 720 O HOH B 795 2.11 REMARK 500 O HOH A 778 O HOH A 818 2.13 REMARK 500 O HOH A 699 O HOH A 856 2.13 REMARK 500 OG1 THR B 289 O HOH B 601 2.14 REMARK 500 OD2 ASP B 282 O HOH B 602 2.14 REMARK 500 OE2 GLU A 338 NH1 ARG A 342 2.15 REMARK 500 O HOH A 747 O HOH B 707 2.16 REMARK 500 O HOH A 674 O HOH A 708 2.16 REMARK 500 O ASP A 151 O HOH A 601 2.16 REMARK 500 O HOH A 770 O HOH A 848 2.16 REMARK 500 O HOH A 660 O HOH B 707 2.17 REMARK 500 O HOH A 840 O HOH A 846 2.18 REMARK 500 O HOH B 731 O HOH B 762 2.18 REMARK 500 O HOH A 686 O HOH A 813 2.18 REMARK 500 O HOH A 792 O HOH A 823 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 810 O HOH B 747 3454 2.16 REMARK 500 O HOH A 807 O HOH B 784 3454 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 VAL B 292 CB VAL B 292 CG2 -0.201 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 VAL B 292 CG1 - CB - CG2 ANGL. DEV. = -11.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 161 -168.49 -127.56 REMARK 500 SER A 227 53.81 37.25 REMARK 500 ILE A 376 -63.04 -130.65 REMARK 500 LEU B 104 132.03 -39.67 REMARK 500 ASN B 161 -166.38 -129.07 REMARK 500 ALA B 180 1.30 -65.33 REMARK 500 LYS B 290 155.51 -49.46 REMARK 500 ILE B 376 -59.36 -125.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 877 DISTANCE = 6.02 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 164 NE2 REMARK 620 2 HIS A 200 NE2 88.0 REMARK 620 3 ASP A 201 OD2 84.7 83.2 REMARK 620 4 ASP A 318 OD1 88.3 86.2 167.5 REMARK 620 5 HOH A 700 O 172.2 95.1 88.5 99.0 REMARK 620 6 HOH A 717 O 88.4 175.8 98.6 91.5 88.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 201 OD1 REMARK 620 2 HOH A 627 O 81.7 REMARK 620 3 HOH A 672 O 166.0 86.6 REMARK 620 4 HOH A 700 O 92.2 92.9 96.2 REMARK 620 5 HOH A 740 O 87.6 90.2 84.6 176.9 REMARK 620 6 HOH A 768 O 105.5 172.5 85.9 88.9 88.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 164 NE2 REMARK 620 2 HIS B 200 NE2 94.6 REMARK 620 3 ASP B 201 OD2 92.7 81.2 REMARK 620 4 ASP B 318 OD1 85.3 87.9 168.8 REMARK 620 5 HOH B 625 O 82.7 176.5 96.7 94.1 REMARK 620 6 HOH B 677 O 167.1 98.3 90.1 94.3 84.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 201 OD1 REMARK 620 2 HOH B 626 O 80.7 REMARK 620 3 HOH B 632 O 166.6 92.1 REMARK 620 4 HOH B 677 O 91.5 103.5 101.1 REMARK 620 5 HOH B 682 O 79.7 90.6 89.2 162.1 REMARK 620 6 HOH B 743 O 95.2 169.7 89.9 86.0 79.3 REMARK 620 N 1 2 3 4 5 DBREF 7W4Y A 78 449 UNP Q08499 PDE4D_HUMAN 380 751 DBREF 7W4Y B 78 449 UNP Q08499 PDE4D_HUMAN 380 751 SEQADV 7W4Y ALA A 450 UNP Q08499 EXPRESSION TAG SEQADV 7W4Y ALA B 450 UNP Q08499 EXPRESSION TAG SEQRES 1 A 373 SER ILE PRO ARG PHE GLY VAL LYS THR GLU GLN GLU ASP SEQRES 2 A 373 VAL LEU ALA LYS GLU LEU GLU ASP VAL ASN LYS TRP GLY SEQRES 3 A 373 LEU HIS VAL PHE ARG ILE ALA GLU LEU SER GLY ASN ARG SEQRES 4 A 373 PRO LEU THR VAL ILE MET HIS THR ILE PHE GLN GLU ARG SEQRES 5 A 373 ASP LEU LEU LYS THR PHE LYS ILE PRO VAL ASP THR LEU SEQRES 6 A 373 ILE THR TYR LEU MET THR LEU GLU ASP HIS TYR HIS ALA SEQRES 7 A 373 ASP VAL ALA TYR HIS ASN ASN ILE HIS ALA ALA ASP VAL SEQRES 8 A 373 VAL GLN SER THR HIS VAL LEU LEU SER THR PRO ALA LEU SEQRES 9 A 373 GLU ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA ILE SEQRES 10 A 373 PHE ALA SER ALA ILE HIS ASP VAL ASP HIS PRO GLY VAL SEQRES 11 A 373 SER ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU ALA SEQRES 12 A 373 LEU MET TYR ASN ASP SER SER VAL LEU GLU ASN HIS HIS SEQRES 13 A 373 LEU ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU ASN CYS SEQRES 14 A 373 ASP ILE PHE GLN ASN LEU THR LYS LYS GLN ARG GLN SER SEQRES 15 A 373 LEU ARG LYS MET VAL ILE ASP ILE VAL LEU ALA THR ASP SEQRES 16 A 373 MET SER LYS HIS MET ASN LEU LEU ALA ASP LEU LYS THR SEQRES 17 A 373 MET VAL GLU THR LYS LYS VAL THR SER SER GLY VAL LEU SEQRES 18 A 373 LEU LEU ASP ASN TYR SER ASP ARG ILE GLN VAL LEU GLN SEQRES 19 A 373 ASN MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR LYS SEQRES 20 A 373 PRO LEU GLN LEU TYR ARG GLN TRP THR ASP ARG ILE MET SEQRES 21 A 373 GLU GLU PHE PHE ARG GLN GLY ASP ARG GLU ARG GLU ARG SEQRES 22 A 373 GLY MET GLU ILE SER PRO MET CYS ASP LYS HIS ASN ALA SEQRES 23 A 373 SER VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR ILE SEQRES 24 A 373 VAL HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL HIS SEQRES 25 A 373 PRO ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP ASN SEQRES 26 A 373 ARG GLU TRP TYR GLN SER THR ILE PRO GLN SER PRO SER SEQRES 27 A 373 PRO ALA PRO ASP ASP PRO GLU GLU GLY ARG GLN GLY GLN SEQRES 28 A 373 THR GLU LYS PHE GLN PHE GLU LEU THR LEU GLU GLU ASP SEQRES 29 A 373 GLY GLU SER ASP THR GLU LYS ASP ALA SEQRES 1 B 373 SER ILE PRO ARG PHE GLY VAL LYS THR GLU GLN GLU ASP SEQRES 2 B 373 VAL LEU ALA LYS GLU LEU GLU ASP VAL ASN LYS TRP GLY SEQRES 3 B 373 LEU HIS VAL PHE ARG ILE ALA GLU LEU SER GLY ASN ARG SEQRES 4 B 373 PRO LEU THR VAL ILE MET HIS THR ILE PHE GLN GLU ARG SEQRES 5 B 373 ASP LEU LEU LYS THR PHE LYS ILE PRO VAL ASP THR LEU SEQRES 6 B 373 ILE THR TYR LEU MET THR LEU GLU ASP HIS TYR HIS ALA SEQRES 7 B 373 ASP VAL ALA TYR HIS ASN ASN ILE HIS ALA ALA ASP VAL SEQRES 8 B 373 VAL GLN SER THR HIS VAL LEU LEU SER THR PRO ALA LEU SEQRES 9 B 373 GLU ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA ILE SEQRES 10 B 373 PHE ALA SER ALA ILE HIS ASP VAL ASP HIS PRO GLY VAL SEQRES 11 B 373 SER ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU ALA SEQRES 12 B 373 LEU MET TYR ASN ASP SER SER VAL LEU GLU ASN HIS HIS SEQRES 13 B 373 LEU ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU ASN CYS SEQRES 14 B 373 ASP ILE PHE GLN ASN LEU THR LYS LYS GLN ARG GLN SER SEQRES 15 B 373 LEU ARG LYS MET VAL ILE ASP ILE VAL LEU ALA THR ASP SEQRES 16 B 373 MET SER LYS HIS MET ASN LEU LEU ALA ASP LEU LYS THR SEQRES 17 B 373 MET VAL GLU THR LYS LYS VAL THR SER SER GLY VAL LEU SEQRES 18 B 373 LEU LEU ASP ASN TYR SER ASP ARG ILE GLN VAL LEU GLN SEQRES 19 B 373 ASN MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR LYS SEQRES 20 B 373 PRO LEU GLN LEU TYR ARG GLN TRP THR ASP ARG ILE MET SEQRES 21 B 373 GLU GLU PHE PHE ARG GLN GLY ASP ARG GLU ARG GLU ARG SEQRES 22 B 373 GLY MET GLU ILE SER PRO MET CYS ASP LYS HIS ASN ALA SEQRES 23 B 373 SER VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR ILE SEQRES 24 B 373 VAL HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL HIS SEQRES 25 B 373 PRO ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP ASN SEQRES 26 B 373 ARG GLU TRP TYR GLN SER THR ILE PRO GLN SER PRO SER SEQRES 27 B 373 PRO ALA PRO ASP ASP PRO GLU GLU GLY ARG GLN GLY GLN SEQRES 28 B 373 THR GLU LYS PHE GLN PHE GLU LEU THR LEU GLU GLU ASP SEQRES 29 B 373 GLY GLU SER ASP THR GLU LYS ASP ALA HET ZN A 501 1 HET MG A 502 1 HET 8GO A 503 26 HET ZN B 501 1 HET MG B 502 1 HET 8GO B 503 26 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM 8GO (2R,4S)-6-ETHYL-2-(2-HYDROXYETHYL)-2,8-DIMETHYL-4-(2- HETNAM 2 8GO METHYLPROP-1-ENYL)-3,4-DIHYDROPYRANO[3,2-C][1, HETNAM 3 8GO 8]NAPHTHYRIDIN-5-ONE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 MG 2(MG 2+) FORMUL 5 8GO 2(C21 H28 N2 O3) FORMUL 9 HOH *480(H2 O) HELIX 1 AA1 GLN A 88 LEU A 96 1 9 HELIX 2 AA2 GLU A 97 VAL A 99 5 3 HELIX 3 AA3 HIS A 105 SER A 113 1 9 HELIX 4 AA4 ARG A 116 ARG A 129 1 14 HELIX 5 AA5 ASP A 130 PHE A 135 1 6 HELIX 6 AA6 PRO A 138 HIS A 152 1 15 HELIX 7 AA7 ASN A 161 SER A 177 1 17 HELIX 8 AA8 THR A 178 GLU A 182 5 5 HELIX 9 AA9 THR A 186 HIS A 200 1 15 HELIX 10 AB1 SER A 208 THR A 215 1 8 HELIX 11 AB2 SER A 217 ASN A 224 1 8 HELIX 12 AB3 SER A 227 LEU A 240 1 14 HELIX 13 AB4 LEU A 241 GLU A 243 5 3 HELIX 14 AB5 THR A 253 ALA A 270 1 18 HELIX 15 AB6 THR A 271 SER A 274 5 4 HELIX 16 AB7 LYS A 275 THR A 289 1 15 HELIX 17 AB8 ASN A 302 LEU A 319 1 18 HELIX 18 AB9 SER A 320 LYS A 324 5 5 HELIX 19 AC1 PRO A 325 ARG A 350 1 26 HELIX 20 AC2 SER A 364 ILE A 376 1 13 HELIX 21 AC3 ILE A 376 VAL A 388 1 13 HELIX 22 AC4 ALA A 392 THR A 409 1 18 HELIX 23 AC5 ASP B 90 GLU B 97 1 8 HELIX 24 AC6 HIS B 105 SER B 113 1 9 HELIX 25 AC7 ARG B 116 ARG B 129 1 14 HELIX 26 AC8 ASP B 130 PHE B 135 1 6 HELIX 27 AC9 PRO B 138 HIS B 152 1 15 HELIX 28 AD1 ASN B 161 SER B 177 1 17 HELIX 29 AD2 THR B 178 GLU B 182 5 5 HELIX 30 AD3 THR B 186 HIS B 200 1 15 HELIX 31 AD4 SER B 208 THR B 215 1 8 HELIX 32 AD5 SER B 217 ASN B 224 1 8 HELIX 33 AD6 SER B 227 LEU B 240 1 14 HELIX 34 AD7 LEU B 241 GLU B 243 5 3 HELIX 35 AD8 THR B 253 ALA B 270 1 18 HELIX 36 AD9 THR B 271 SER B 274 5 4 HELIX 37 AE1 LYS B 275 THR B 289 1 15 HELIX 38 AE2 ASN B 302 LEU B 319 1 18 HELIX 39 AE3 SER B 320 LYS B 324 5 5 HELIX 40 AE4 PRO B 325 ARG B 350 1 26 HELIX 41 AE5 SER B 364 ILE B 376 1 13 HELIX 42 AE6 ILE B 376 VAL B 388 1 13 HELIX 43 AE7 ALA B 392 THR B 409 1 18 LINK NE2 HIS A 164 ZN ZN A 501 1555 1555 2.21 LINK NE2 HIS A 200 ZN ZN A 501 1555 1555 2.24 LINK OD2 ASP A 201 ZN ZN A 501 1555 1555 2.09 LINK OD1 ASP A 201 MG MG A 502 1555 1555 2.16 LINK OD1 ASP A 318 ZN ZN A 501 1555 1555 2.18 LINK ZN ZN A 501 O HOH A 700 1555 1555 2.04 LINK ZN ZN A 501 O HOH A 717 1555 1555 2.20 LINK MG MG A 502 O HOH A 627 1555 1555 2.27 LINK MG MG A 502 O HOH A 672 1555 1555 2.18 LINK MG MG A 502 O HOH A 700 1555 1555 2.05 LINK MG MG A 502 O HOH A 740 1555 1555 2.05 LINK MG MG A 502 O HOH A 768 1555 1555 2.13 LINK NE2 HIS B 164 ZN ZN B 501 1555 1555 2.28 LINK NE2 HIS B 200 ZN ZN B 501 1555 1555 2.21 LINK OD2 ASP B 201 ZN ZN B 501 1555 1555 2.05 LINK OD1 ASP B 201 MG MG B 502 1555 1555 2.13 LINK OD1 ASP B 318 ZN ZN B 501 1555 1555 2.10 LINK ZN ZN B 501 O HOH B 625 1555 1555 2.37 LINK ZN ZN B 501 O HOH B 677 1555 1555 2.03 LINK MG MG B 502 O HOH B 626 1555 1555 2.18 LINK MG MG B 502 O HOH B 632 1555 1555 2.11 LINK MG MG B 502 O HOH B 677 1555 1555 2.00 LINK MG MG B 502 O HOH B 682 1555 1555 2.32 LINK MG MG B 502 O HOH B 743 1555 1555 2.00 CISPEP 1 HIS A 389 PRO A 390 0 4.46 CISPEP 2 HIS B 389 PRO B 390 0 6.80 CRYST1 58.294 80.834 163.423 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017154 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012371 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006119 0.00000